+\subsection{File - Properties}
+Properties of image files include:
+\begin{itemize}\itemsep=0pt
+ \item Whether the image is real or complex-valued.
+ \item Numeric statistics (minimum, maximum, mean, median, mode, and standard deviation).
+ \item History labels (text descriptions of the processing for this image).
+\end{itemize}
+
+\subsection{File - Export}\label{IDH_DLG_EXPORT}\index{Image!Export}
+This command allows for exporting image files to a standard
+graphics file format. This is helpful when you want to take an
+image and import it into another application. The current
+\helprefn{intensity scale}{intensityscale} is used when exporting
+the file. The supported graphic formats are:
+
+\begin{twocollist}
+\twocolitem{\textbf{PNG}}{Portable Network Graphics format. This uses 8-bits or
+256 shades of gray.}
+\twocolitem{\textbf{PNG-16}}{This is a 16-bit version of PNG which allows for
+65536 shades of gray.}
+\twocolitem{\textbf{PGM}}{Portable Graymap format. This is a common format used on
+UNIX systems.}
+\twocolitem{\textbf{PGM ASCII}}{ASCII version of PGM.}
+\end{twocollist}
+
+
+\subsection{View}
+\subsubsection{Intensity Scale}\label{intensityscale}\index{Intensity scale}
+These commands are used change the intensity scale for viewing the image.
+These commands do not change the image data. When the minimum value is
+set, then the color pure black is assigned to that image value. Similarly,
+when the maximum value is set, the the color pure white is assigned to that
+image value.
+
+Changing the intensity scale is useful when examining different image features.
+In clinical medicine, the intensity scale is often changed to examine bone
+(high value) versus soft-tissue (medium value) features.
+
+\subsubsection{Set}\label{IDH_DLG_MINMAX}
+This command displays a dialog box that sets the lower
+and upper values to display.
+
+\subsubsection{Auto}\label{IDH_DLG_AUTOSCALE}\index{Auto scale}
+This command displays a dialog box that allows \ctsim\ to automatically
+make an intensity scale. The parameters that \ctsim\ needs to make this
+automatic scale are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Center}}{This sets the center of the intensity scale. Currently,
+\ctsim\ allows you to use either the mean, mode, or median of the image
+as the center of the intensity scale.}
+
+\twocolitem{\textbf{Width}}{This sets the half-width of the intensity scale. The half-width
+is specified as a multiple of the standard deviation.}
+\end{twocollist}
+
+As an example, if \texttt{median} is selected as the center and
+\texttt{0.5} is selected as the width, the the minimum value will
+be \latexonly{$median - 0.5 \times standardDeviation$}\latexignore{\emph{median - 0.5 x standardDeviation}}
+and the maximum value will be \latexonly{$median + 0.5 \times standardDeviation$.}\latexignore{\emph{
+median + 0.5 x standardDeviation}.}
+
+\subsubsection{Full}
+This command resets the intensity scale to the full scale of the image.
+
+\subsection{Image}
+These commands create a new image based upon the current image,
+and for some commands, also upon a comparison image.
+
+\subsubsection{Add, Subtract, Multiply, Divide}
+These are simple arithmetic operations. \ctsim\ will display a dialog
+box showing all of the currently opened image files that are the
+same size as the active image. After the selection of a compatible image,
+\ctsim\ will perform the arithmetic operation on the two images and
+make a new result image.
+
+\subsubsection{Image Size}
+This command will generate a new image based on the current image. The new
+image can be scaled to any size. A dialog
+appears asking for the size of the new image. Bilinear interpolation
+is used when calculating the new image.
+
+\subsubsection{3-D Conversion}
+This command generates a 3-dimensional view of the current phantom. This view can be
+rotated in three dimensions. The left and right arrow control the z-axis
+rotation and the up and down arrows control the x-axis rotation. The y-axis
+rotation is controlled by the \texttt{T} and \texttt{Y} keys. Other options
+are presented on the \texttt{View} menu and include:
+
+\begin{itemize}\itemsep=0pt
+\item Surface plot versus wireframe plot.
+\item Smooth shading versus flat shading.
+\item Lighting on or off.
+\item Color scale on or off.
+\end{itemize}
+
+\subsection{Filter}\index{Image!Filter}
+These commands filter and modify the image
+
+\subsubsection{Arithmetic}
+These commands operate on the image on a pixel-by-pixel basis. The commands
+support both real and complex-valued images. The available arithmetic commards are:
+
+\begin{twocollist}
+ \twocolitem{\textbf{Invert}}{Negate pixel values.}
+ \twocolitem{\textbf{Log}}{Take natural logrithm of pixel values.}
+ \twocolitem{\textbf{Exp}}{Take natural exponent of pixel values.}
+ \twocolitem{\textbf{Square}}{Take square of pixel values.}
+ \twocolitem{\textbf{Square root}}{Take square root of pixel values.}
+\end{twocollist}
+
+
+\subsubsection{Frequency Based}
+These commands perform Fourier and inverse Fourier transformations of
+images. By default, the transformations will automatically convert
+images between Fourier to natural orders as expected. For example, \texttt{2-D FFT}
+will transform the points into natural order after the Fourier transform.
+Similarly the inverse, \texttt{2-D IFFT}, will reorder the points from
+natural order to Fourier order before applying the inverse Fourier transformation.
+
+As you would expect, images that undergo frequency filtering will be complex-valued
+after than filtering. Only the real component is shown by \ctsim. However, \ctsim\ does
+have options for converting a complex-valued image into a real-valued image via
+the \texttt{Magnitude} and \texttt{Phase} filtering commands.
+
+The available frequency-based filtering commards are:
+
+\begin{itemize}\itemsep=0pt
+\item 2-D FFT
+\item 2-D IFFT
+\item FFT Rows
+\item IFFT Rows
+\item FFT Columns
+\item IFFT Columns
+\item 2-D Fourier
+\item 2-D Inverse Fourier
+\item Shuffle Fourier to Natural Order
+\item Shuffle Natural to Fourier Order
+\item Magnitude
+\item Phase
+\end{itemize}
+
+\subsection{Analyze - Plot}
+The commands plot rows and columns of images. There are commands
+that perform FFT transformations prior to plotting. To select
+the row or column to plot, click the left mouse button over the
+desired cursor point.
+
+The available plot commands are:
+\begin{itemize}\itemsep=0pt
+\item Plot Row
+\item Plot Column
+\item Plot Histogram
+\item Plot FFT Row
+\item Plot FFT Col
+\end{itemize}
+
+\subsection{Analyze - Compare}\label{IDH_DLG_COMPARISON}\index{Image!Comparison}
+This command performs statistical comparisons between two images. An option
+also exists for generating a difference image from the two input images.
+
+The three distance measures reported are:
+\begin{itemize}\itemsep=0pt
+\item[] \textbf{$d$}\quad The normalized root mean squared distance measure.
+\item[] \textbf{$r$}\quad The normalized mean absolute distance measure.
+\item[] \textbf{$e$}\quad The worst case distance measure over a \latexonly{$2\times2$}\latexignore{\emph{2 x 2}} pixel area.
+\end{itemize}
+
+There are also commands for comparison plotting of rows and columns from two images.
+This is quite helpful when comparing a phantom to a reconstruction. As with plotting
+of rows and columns, click the left mouse button over the desired cursor point to
+choose which row and column to plot.
+